At the moment, raster animations are only possible with animated GIFs which support just 1 bit transparency. Other possibilities just aren't sufficient, both Flash and SVG are vector-based and not always appropriate.
Note: I personally do not care much about the patent issues that seemed relevant to the GIF debate of years gone by, and besides, I believe those patents have all expired recently.
An alternative might be the APNG format, but I do not consider myself qualified to weigh the advantages and disadvantages of MNG vs. APNG.

We usually rely on platform frameworks (such as ImageIO on the Mac) to do image decoding, so most of the work is outside WebKit - but some minor adaptation will still be needed, of course.
Someone has already filed an enhancement request with Apple for MNG support. You may want to file a duplicate (<http://bugreport.apple.com>, free registration required), describing your specific needs and use cases, to make sure they are accounted for.

(In reply to comment #4)
> It's bug number 4855683. I didn't realize my link was bad, sorry. I can't
> figure out a link that's not account dependent. Logging out blocks you from
> seeing bugs, so...
The bugreport.apple.com site is designed so you can't link to bugs--radar bugs are considered private to the person who reports them. The best you can do is just report the bug number here so Apple employees may view to them (or others filing their own radar bugs may reference the bug number).
Note that if <rdar://problem/4855683> hasn't been marked a duplicate, then you were probably the first one to report the issue.
Also note that for non-Mac OS X versions of WebKit, libmng will need to be integrated into WebKit (WebCore/platform/image-decoders).